The environment commissioner works in the Office of the Auditor General, so it shouldn't change the royal recommendation that we've already received. As to whether or not the amended version of a bill can be requested for another royal recommendation, I think that would be up to the parties rather than the committee.
Let me read this from June 15. This is the ruling by Speaker Milliken on Bill C-469:
As the member for Edmonton—Strathcona pointed out, the Office of the Auditor General includes the position of Commissioner of the Environment, who reports to Parliament through the Auditor General. The Commissioner is given a broad mandate with respect to the content of that office’s reports, as set out in paragraph 23(2) of the Act, which reads, in part: “The Commissioner shall, on behalf of the Auditor General, report annually to the House of Commons concerning anything that the Commissioner considers should be brought to the attention of the House in relation to environmental and other aspects of sustainable development....”
Then it goes on:
The provisions of Bill C-469 concerning the Auditor General are limited to the examination of federal bills and regulations. Here again, it does not appear that the bill broadens the mandate of the commissioner, nor does it require the commissioner to undertake any work not already within his purview. In conclusion, the Chair is unable to find any authorization for a new expenditure of public funds in Bill C-469, nor does the bill appear to assign any function to the Office of the Auditor General that goes beyond the existing mandate of that office. I therefore rule that Bill C-469 does not infringe on the financial initiative of the Crown and so does not require a royal recommendation.
So I think that would stand, since the environment commissioner works out of the AG's office.